title: Nucleotide sequence alignment using sparse coding and belief propagation.
abstract: Advances in DNA information extraction techniques have led to huge sequenced genomes from organisms spanning the tree of life. This increasing amount of genomic information requires tools for comparison of the nucleotide sequences. In this paper, we propose a novel nucleotide sequence alignment method based on sparse coding and belief propagation to compare the similarity of the nucleotide sequences. We used the neighbors of each nucleotide as features, and then we employed sparse coding to find a set of candidate nucleotides. To select optimum matches, belief propagation was subsequently applied to these candidate nucleotides. Experimental results show that the proposed approach is able to robustly align nucleotide sequences and is competitive to SOAPaligner [1] and BWA [2].
authors.forename: Aminmohammad
authors.initials: A
authors.lastname: Roozgard
authors.forename: Nafise
authors.initials: N
authors.lastname: Barzigar
authors.forename: Shuang
authors.initials: S
authors.lastname: Wang
authors.forename: Xiaoqian
authors.initials: X
authors.lastname: Jiang
authors.forename: Lucila
authors.initials: L
authors.lastname: Ohno-Machado
authors.forename: Samuel
authors.initials: S
authors.lastname: Cheng
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002877:Chromosomes, Human / Q000235:genetics; D006801:Humans; D016415:Sequence Alignment / Q000379:methods*